BamUtil¶
BamUtil is a collection of programs that perform operations on SAM and BAM files.
BamUtil is available as a module on Apocrita.
Usage¶
To run the default installed version of BamUtil, simply load the bamutil
module:
module load bamutil
For usage documentation, run bam -h.
Example jobs¶
Serial jobs¶
Here is an example job to clip overlapping read pairs, running on 1 core and 1GB of memory:
#!/bin/bash
#$ -cwd
#$ -j y
#$ -pe smp 1
#$ -l h_rt=1:0:0
#$ -l h_vmem=1G
module load bamutil
bam clipOverlap --in example.bam \
--out clipped.bam
Here is an example job to validate and check a BAM file format (also works for SAM files) and printing verbose statistics, running on 1 core and 1GB memory:
#!/bin/bash
#$ -cwd
#$ -j y
#$ -pe smp 1
#$ -l h_rt=1:0:0
#$ -l h_vmem=1G
module load bamutil
bam validate --in example.bam \
--verbose